title: MODBASE, a database of annotated comparative protein structure models and associated resources.
abstract: MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Narayanan
authors.initials: N
authors.lastname: Eswar
authors.forename: Ben M
authors.initials: BM
authors.lastname: Webb
authors.forename: David
authors.initials: D
authors.lastname: Eramian
authors.forename: Libusha
authors.initials: L
authors.lastname: Kelly
authors.forename: David T
authors.initials: DT
authors.lastname: Barkan
authors.forename: Hannah
authors.initials: H
authors.lastname: Carter
authors.forename: Parminder
authors.initials: P
authors.lastname: Mankoo
authors.forename: Rachel
authors.initials: R
authors.lastname: Karchin
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins